How do I manually set the value of a custom EnumProperty in python?
Check if a bpy.prop property has been initialized by looking at its custom property "data store".

Have a look at the Getter / Setter examples for bpy.props.  The ENUM_FLAG option enum property is saved internally as a custom property of the same name,  an integer, calculated from each item having an "internal id" of a power of 2 (aka bitwise). 1, 2, 4, 8...  The empty set set() 0, first only 1, first and second 1 | 2, and third 1 | 2 | 4 ...

As an example I've used the items method to show how to alter the data store (the custom property) only if it hasn't been already set.  I've used a scene bool to emulate the addon prefs boolean. 

import bpy
from bpy.props import BoolProperty, EnumProperty


def channel_items(self, context):
    prefs = context.scene    

    red_id, green_id, blue_id, alpha_id = (c for c in "rgba")
    items = [(red_id, "R", ""),
            (green_id, "G", ""), 
            (blue_id, "B", "")]
    if prefs.alpha_support:
        items.append((alpha_id, "A", ""))

    if not self.get("active_channels"):
        self["active_channels"] = 1 | 2 | 4 #rgb
        if prefs.alpha_support:
            self["active_channels"] |= 8

    return items

def update_rgba(self, context):
    print("enum set", self.active_channels, "int", self["active_channels"])
    return None

active_channels = EnumProperty(
    name="Active Channels",
    options={'ENUM_FLAG'},
    items=channel_items,
    update=update_rgba,
)
bpy.types.Scene.active_channels = active_channels
bpy.types.Scene.alpha_support = BoolProperty(default=False)


Note the above will give all for empty selection, as well as the custom property not being set.  To check if bpy.prop is initialized would use

is_init = self.get("active_channels") is not None